Atomic scale simulations

C. C. Battaille, D. J. Srolvitz, J. E. Butler. A kinetic Monte Carlo method for the atomic-scale simulation of chemical vapor deposition application to diamond. J App Phys 52 6293, 1997. 

Ab initio methods allow the nature of active sites to be elucidated and the influence of supports or solvents on the catalytic kinetics to be predicted. Neurock and coworkers have successfully coupled theory with atomic-scale simulations and have tracked the molecular transformations that occur over different surfaces to assess their catalytic activity and selectivity [95-98]. Relevant examples are the Pt-catalyzed NO decomposition and methanol oxidation. In case of NO decomposition, density functional theory calculations and kinetic Monte Carlo simulations substantially helped to optimize the composition of the nanocatalyst by alloying Pt with Au and creating a specific structure of the PtgAu7 particles. In catalytic methanol decomposition the elementary pathways were identified... 

Bhushan, Ed., CRC Press, Boca Raton, FL, 1999, pp. 525—597. Atomic-Scale Simulations of Tribological and Related Phenomena. 

H. Camon and Z. Moktadir, Atomic scale simulation of silicon etched in aqueous KOH solution, Sensors Actuators A 46, 27, 1995. 

Fig. 2. Two-dimensional illustration of the geometric definition of the pore size distribution [25]. Point Z may be overlapped by all three circles of differing radii, whereas point Y is accessible only to the two smaller circles and point X is excluded from all but the smallest circle. The geometric pore size distribution is obtained by determining the size of the largest circle that can overlap each point in the pore volume. (Reproduced with permission from S. Ramalingam, D. Maroudas. and E. S. Aydil. Interactions of SiH radicals with silicon surfaces An atomic-scale simulation study. Journal of Applied Physics, 1998 84 3895-3911. Copyright 1998, American Institute of Physics.)...

Several empirical and semiempirical interatomic potentials have been developed for the Si H systembased on extensions and modifications of well-known potentials for Si including up to three-body interactions (StilUnger and Weber, 1985 Biswas and Hamann, 1985 Biswas et al., 1987 Mousseau and Lewis, 1991 Baskes, 1992). Recent atomic-scale simulation work of plasma-surface interactions in the PECVD of Si thin films has been based on an empirical description of interatomic interactions in the Si H system according to Tersoff s (1986, 1988, 1989) potential for Si, as extended by Ohira and co-workers (1994, 1995, 1996) to incorporate Si-H, H-H, and the corresponding three-body interactions. The extension of the potential to include the presence of hydrogen adopted the Tersoff parametrization to fit results of ab initio calculations for the structure and energetics of Sil 1., x <4, species in the gas phase (Ohira et al., 1994,1995,1996). A similar form of... 

Battaile, C. C, Srolovitz, D. J., and Butler, J. E., Atomic-scale simulations of chemical vapor deposition on flat and vicinal diamond substrates. 7. Crystal Growth 194, 353-368 (1998). 

Ramalingam, S., Maroudas, D., and Aydil. E. S.. Interactions of SiHradicals with silicon surfaces An atomic-scale simulation study. J. Appl. Phys. 84,3895-3911 (1998b). 

Gurtovenko AA, Vattulainen I (2008) Effect of NaCl and KCl on phosphatidylcholine and phosphatidyleth-anolamine lipid membranes insight from atomic-scale simulations for understanding salt-induced effects in the plasma membrane. J Phys Chem B 112 1953-1962... 

The status of computer simulations of electric double layers is briefly summarized and a road map for solving the important problems in the atomic scale simulation of interfacial electrochemical processes is proposed. As examples efforts to simulate screening in electric double layers are described. Molecular dynamics simulations on systems about 4 nm thick, containing up to 1600 water molecules and NaQ at IM to 3M concentration, displayed the main features of double layers at charged metal surfaces including bulk electrolyte zone, diffuse ionic layer that screens the charge on the electrode and a layer of oriented water next to the surface. 

Harrison, J. A. Stuart, S. J. Brenner, D. W. In Handbook of Micro/Nanotribology, 2nd edition, Ed. Bhushan, B. CRC Press Boca Raton, FL, 1999 Chapter 11 "Atomic-Scale Simulation of Tribological and Related Phenomena", pp. 525-594 and references therein. 

The Free Software project for Atomic-scale Simulation aims at spreading the use of free software in atomic-scale simulations (URL http //www. f satom. org). 

This is where computer simulations come into play. The time and space resolution of atomic-scale simulations can hardly be achieved through any other methods. The models are able to reveal elusive structural and dynamical features of a biomaterial... 

In atomic scale simulations, there is often a clear separation of timescales. The rate of rare events, e.g., chemical reactions, in a system coupled to a heat bath can be estimated by evaluating the free energy barriers for the transitions. Transition State Theory (TST) [9] is the foundation for this approach. Due to the large difference in time scale between atomic vibrations and typical thermally induced processes such as chemical reactions or diffusion, this would require immense computational power to directly simulate dynamical trajectories for a sufficient period of time to include these rare events. Identification of transition states is often the critical step in assessing rates of chemical reactions and path techniques like the nudged elastic band method is often used to identify these states [10-12,109]. 

The first developed a mathematical model to relate Young s modulus to polymer chain scission and is based on entropy theory for rubber elasticity. The second was an MD study of the effect of chain scission on Young s modulus in a semi-crystalline polymer. The third study developed a model to relate Young s modulus to polymer chain scission, and is based on atomic-scale simulations for glassy polymers. 

C. C. Battaile, D. J. Srolovitz, and J. E. Butler,/. Appl. Phys., 82, 6293 (1997). A Kinetic Monte Carlo Method for the Atomic-Scale Simulation of Chemical Vapor Deposition Application to Diamond. 

Neyts EC, Van Duin ACT, Bogaerts A (2012) Insights in the plasma-assisted growth of carbon nanotubes through atomic scale simulations effect of electric field. J Am Chem Soc 134(2) 1256-1260... 

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